Research workbench
Crystal structure of a T.THERMOPHILUS HB8 AP6A hydrolase E50Q mutant- MG2+-ATP complex
Analyse Crystal structure of a T.THERMOPHILUS HB8 AP6A hydrolase E50Q mutant- MG2+-ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VC9
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NDX1
- UniProt
- Q75UV1
- Ligands
- ATP, MG
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NDX1 | protein | 126 | 26% helix, 34% strand | Q75UV1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.58 | 0.78 | 32 | ATP |
| 2 | 238 | 0.53 | 0.76 | 27 | ATP |
Interfaces
1 interface between chains.
- A–B · 662 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1VC9 · Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase E50Q mutant-Mg2+-ATP complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q75UV1 · AlphaFold monomer V2.0 prediction for diadenosine hexaphosphate hydrolase (Q75UV1) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q75UV1
- Elsewhere: RCSB PDB 1VC9 · PDBe 1VC9 · UniProt Q75UV1
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